[med-svn] r15920 - trunk/packages/flexbar/trunk/debian/patches

[Andreas Tille]

Author: tille
Date: 2014-01-31 12:02:36 +0000 (Fri, 31 Jan 2014)
New Revision: 15920

Removed:
   trunk/packages/flexbar/trunk/debian/patches/removerpath.patch
Modified:
   trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch
   trunk/packages/flexbar/trunk/debian/patches/series
Log:
Adapt patches to latest upstream version


Modified: trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch
===================================================================
--- trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch	2014-01-31 11:50:37 UTC (rev 15919)
+++ trunk/packages/flexbar/trunk/debian/patches/add_shebang_to_tests.patch	2014-01-31 12:02:36 UTC (rev 15920)
@@ -1,5 +1,5 @@
 Author: Andreas Tille <tille at debian.org>
-Date: Thu, 13 Jun 2013 13:02:17 +0200
+Date: Fri, 31 Jan 2014 12:55:18 +0100
 Description: Add shebang line for shell scripts
 
 --- a/test/flexbar_test_csfasta.sh
@@ -7,33 +7,33 @@
 @@ -1,4 +1,4 @@
 -
 +#!/bin/sh
- flexbar --reads test.csfasta --target result_right_nw --format csfasta --adapter-min-overlap 4 --adapters adapters_cs.fasta --min-readlength 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
+ flexbar --reads test.csfasta --target result_right --format csfasta --adapter-min-overlap 4 --adapters adapters_cs.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
- a=`diff correct_result_right_nw.csfasta result_right_nw.csfasta`
+ a=`diff correct_result_right.csfasta result_right.csfasta`
 --- a/test/flexbar_test_csfastq.sh
 +++ b/test/flexbar_test_csfastq.sh
 @@ -1,4 +1,4 @@
 -
 +#!/bin/sh
- flexbar --reads test.csfastq --target result_right_nw --format csfastq --adapter-min-overlap 4 --adapters adapters_cs.fasta --min-readlength 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
+ flexbar --reads test.csfastq --target result_right --format csfastq --adapter-min-overlap 4 --adapters adapters_cs.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
- a=`diff correct_result_right_nw.csfastq result_right_nw.csfastq`
+ a=`diff correct_result_right.csfastq result_right.csfastq`
 --- a/test/flexbar_test_fasta.sh
 +++ b/test/flexbar_test_fasta.sh
 @@ -1,4 +1,4 @@
 -
 +#!/bin/sh
- flexbar --reads test.fasta --target result_right_nw --format fasta --adapter-min-overlap 4 --adapters adapters.fasta --min-readlength 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
+ flexbar --reads test.fasta --target result_right --format fasta --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
- a=`diff correct_result_right_nw.fasta result_right_nw.fasta`
+ a=`diff correct_result_right.fasta result_right.fasta`
 --- a/test/flexbar_test_fastq.sh
 +++ b/test/flexbar_test_fastq.sh
 @@ -1,4 +1,4 @@
 -
 +#!/bin/sh
- flexbar --reads test.fastq --target result_right_nw --format fastq-illumina1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-readlength 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
+ flexbar --reads test.fastq --target result_right --format fastq-i1.5 --adapter-min-overlap 4 --adapters adapters.fasta --min-read-length 10 --adapter-threshold 1 --adapter-trim-end RIGHT > /dev/null
  
- a=`diff correct_result_right_nw.fastq result_right_nw.fastq`
+ a=`diff correct_result_right.fastq result_right.fastq`
 --- a/test/flexbar_validate.sh
 +++ b/test/flexbar_validate.sh
 @@ -1,4 +1,4 @@

Deleted: trunk/packages/flexbar/trunk/debian/patches/removerpath.patch
===================================================================
--- trunk/packages/flexbar/trunk/debian/patches/removerpath.patch	2014-01-31 11:50:37 UTC (rev 15919)
+++ trunk/packages/flexbar/trunk/debian/patches/removerpath.patch	2014-01-31 12:02:36 UTC (rev 15920)
@@ -1,12 +0,0 @@
-Author: Andreas Tille <tille at debian.org>
-Date: Sat, 23 Feb 2013 19:24:05 +0000
-LastChanged: Thu, 13 Jun 2013 13:02:17 +0200
-Description: Make sure that rpath is not uselessly set
-
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -1,3 +1,4 @@
-+set(CMAKE_SKIP_RPATH ON CACHE INTERNAL "" FORCE)
- 
- INCLUDE_DIRECTORIES(${FLEXBAR_SOURCE_DIR}/include)
- 

Modified: trunk/packages/flexbar/trunk/debian/patches/series
===================================================================
--- trunk/packages/flexbar/trunk/debian/patches/series	2014-01-31 11:50:37 UTC (rev 15919)
+++ trunk/packages/flexbar/trunk/debian/patches/series	2014-01-31 12:02:36 UTC (rev 15920)
@@ -1,2 +1 @@
-# removerpath.patch
-# add_shebang_to_tests.patch
+add_shebang_to_tests.patch